William E. Holben - US grants

0120735
Holben

More than a century of metal mining in the Northwest region of the U.S. has created numerous open water extreme environments with unusual metal and chemical composition. In addition to their status as Superfund sites, these environments also represent large-scale outdoor laboratories in which it is highly likely that unusual biogeochemical cycles and microbial metabolic strategies exist. We are requesting one year of funding through the SGER component of this program to facilitate development of a multidisciplinary, polyphasic approach that is generally applicable to resolving the chemical and biological components of biogeochemical cycling in a series of these extreme and unusual aquatic environments that vary in key biogeochemical parameters.
Considering the unique nature of these environments, and the paucity of information on the biological component of the biogeochemical cycles, preliminary fundino, is necessary to develop appropriate sampling strategies, equipment and analytical techniques, assemble the requisite expertise, determine the key parameters to measure, and develop a model framework adequate for dealing with a suite of extreme aquatic environments proposed for future study. The requested year of funding will provide preliminary data, methodologies, and demonstration of feasibility that will allow us to prepare a full proposal for the 2002 Biocomplexity Program Call.

Charcoal is a natural byproduct of wildland and prescribed fire and is well known as an important biochemical sorbent. Unfortunately, charcoal deposited during fire has received little scientific attention. Ponderosa pine forests are fire dependent ecosystems that are notoriously limited in productivity due to low nitrogen (N) availability. Fire results in a short-term increase in available N, but it appears that charcoal may dictate long-term N availability. We will determine whether charcoal directly or indirectly enhances forest N fertility. We will combine state-of-the-art soil microbiological and biochemical methodologies with fire history research plots (USDA-NRI project) to assess the influence of fire and fire exclusion on quantity and biophysical quality of charcoal. The experiments will provide the first ever look at charcoal as a mediator of nutrient dynamics in the Inland Northwest and are likely to have broad impact as fire and charcoal are common to all temperate ecosystems.

Drs. James Gannon, William Holben, Jack Stanford and William Woessner of the University of Montana have been funded to establish the Nyack Microbial Observatory project. Beginning in the Bob Marshall Wilderness of Montana and the southern part of Glacier National Park, the Middle Fork of the Flathead River flows through narrow canyons until it reaches the glacier-carved Nyack Flood Plain. The floodplain is home to numerous wildlife species, including threatened grizzly bear, gray wolf, and bull trout, but their invisible essential partners, the microbes, are no less important. As the river enters the upstream end of the valley, 30 percent of the flow enters a shallow aquifer (hyporheic) before eventually re-entering to the river channel down stream. An abundance of large-bodied insects with life cycle stages uniquely tied to the hyporheic habitat have been discovered here. This terrestrial to aquatic interface can be visualized as a pristine food web where nutrients washed from the forest floor are "re-packaged" into microorganisms and then transferred to aquatic insects, which, in turn, are consumed by fish, and so on up the food chain. Hyporheic habitats, found throughout the world, are critical to nutrient cycles that maintain and rejuvenate all of life in the river corridor. Despite their importance, the microorganisms of the hyporheos are largely unknown. Understanding who they are and what controls their diversity and abundance is the overarching goal of the Nyack Microbial Observatory.

A separate NSF Biocomplexity project has mapped the Nyack hyporheic boundary in 3 dimensions and has installed approximately 100 sampling wells. Using this infrastructure, the Nyack Microbial Observatory will explore the hyporheic community to quantify, cultivate, and characterize novel microorganisms and measure factors that shape the microbial community and link microbial diversity to higher organisms. We seek a broader understanding of floodplain/river health as mediated by flux of water and materials through the river and its floodplain aquifer. The 5 year project will use a suite of innovative molecular, microbiological, and hydrological tools to monitor microbial communities across seasons and along this unique hyporheic gradient. It will also strengthen ties between microbiologists and ecosystem scientists so that they can better understand organismal interactions and processes across many scales. Undergraduate and graduate students alike will be trained in a multidisciplinary environment in which microbial diversity science is closely linked to geology, landscape ecology and ecosystem function.

This IGERT award establishes the Montana Ecology of Infectious Disease (M-EID) program at the University of Montana. The program focus on ecology of infectious diseases addresses the need to train leaders in an emerging field of global and local importance with considerable scientific, societal, ethical and policy aspects. M-EID has three major components: 1) interdisciplinary, team-based training in mathematics, computation, and biology; 2) specific training in establishing collaboration, team-building, and effective communication among disciplines and to other societal sectors; 3) professional development and career enhancement. M-EID faculty are from mathematical, computational, ecosystem, and biological sciences. The main research focus areas encompass different temporal and spatial scales and different levels of biological organization, providing fertile ground for innovation in mathematics and computer science at the interface of biology. Through an interwoven curriculum and guided application and experimentation, M-EID trainees will develop expertise in a primary discipline that will be applied to an interdisciplinary research problem. Trainees will have explicit training in team building, communication across the sciences, and effective teaching. M-EID has relationships with individuals, institutions, and agencies in the U.S. and abroad providing Fellows with additional venues to develop academic excellence and career opportunities. M-EID focuses on recruitment of Native Americans and other underrepresented groups through ties with tribal colleges and undergraduate summer institutes serving minorities and women. This program will serve as a model for small- to mid-sized institutions in effective interdisciplinary graduate education emphasizing both academic excellence and effective collaborative and communication skills. IGERT is an NSF-wide program intended to meet the challenges of educating U.S. Ph.D. scientists and engineers with the interdisciplinary background, deep knowledge in a chosen discipline, and the technical, professional, and personal skills needed for the career demands of the future. The program is intended to catalyze a cultural change in graduate education by establishing innovative new models for graduate education and training in a fertile environment for collaborative research that transcends traditional disciplinary boundaries.

The Division of Biological Sciences at the University of Montana is offering an 8-week summer REU program for eight undergraduate students, including incoming freshmen. Students with an interest in environmental biology will be recruited. Students will be matched with a mentor based on their interests and will conduct an original hands-on research in one of the areas offered in the program, which include microbial ecology, plant ecology, and ecological and evolutionary genetics. Student projects will be designed to help REU participants develop their research skills and independence, as well as enhance their knowledge in a specific area of environmental biology. Students will gain experience in many aspects of scientific research, including formulating questions and hypotheses; designing experiments; analyzing data; writing a paper, and communicating research results. Students will also participate in workshops to develop additional research-related skills, to learn about career options in environmental biology, and to learn how research findings are applied in areas such as ecology of disease, habitat restoration, wildlife management, forest management, and invasive species management. Students will also have the opportunity to share their experience in group meetings and to develop a sense of scientific community. Applications from graduating high school seniors and from Native American students are encouraged. More information is available at http://reu.dbs.umt.edu or by contacting Bill Holben at bill.holben@mso.umt.edu, or (406) 243-6163.

A Research Experience for Undergraduates (REU) Sites award has been made to the University of Montana that will provide research training for ten students, for nine weeks during the summers of 2012- 2014. This REU site, and its collaboration with the Universidad Autonoma de Chihuahua in Mexico, is supported by the NSF's Office of International Science and Engineering (OISE) and the Directorate for Biological Sciences (BIO). Our REU program, the Introductory Multicultural Summer Undergraduate Research Experience (IM-SURE) Program is administered through the Division of Biological Sciences. IM-SURE is primarily intended for undergraduate students (including college-bound high school graduates) nationwide who are interested in environmental biology, but have had little or no research experience to date. Each student will conduct original hands-on research under the guidance of a faculty member and her/his research group. Major areas of research include microbial ecology, plant ecology, and ecological and evolutionary genetics. Students will be matched with a research mentor and project based on their interests, skills, and experience. Projects will be designed to help students develop their research skills and independence, as well as their knowledge of a specific area of environmental biology. REU researchers may be placed on the UM campus (or associated field sites), at UM?s Flathead Lake Biological Station, or, for select students with some prior experience, at our partner institution in Chihuahua, Mexico (along with a UM mentor). Students will gain experience in a variety of aspects of scientific research, such as formulating research questions and hypotheses; designing experiments; analyzing data; and communicating research results. Initial orientation, midsummer social activities, and capstone meetings of the entire group will offer opportunities for IM-SURE students to share their experience and develop a sense of scientific community. We seek to provide a collegial and supportive environment for all participants and measure our success and student satisfaction and accomplishments through the national REU Assessment Tool (URSSA) and our own brief surveys. Students are tracked to determine their continued interest in their academic field of study, their career paths, and the lasting influences of their research experience. IM-SURE participants are selected based on academic record, personal interest statement, research experience essay (although prior experience is not required), and two reference letters. We especially encourage applications from graduating high school seniors, Native American students and other underrepresented groups in science, technology, engineering and math (STEM). For more information, visit or contact the IM-SURE PI (Dr. William Holben at im-sure@mso.umt.edu), or phone (406) 243-5670.

DESCRIPTION (provided by applicant): One barrier that all disease-causing organisms must overcome in order to affect their host is that of microbial communities that live on and within the host (the host microbiome). Yet most studies of infectious disease fail to examine associations between pathogens and the microbiome. Here, we propose using Clostridium difficile as a model for examining how an opportunistic pathogen either causes or takes advantage of changes in the intestinal microbiome to infect the host and cause disease. C. difficile causes serious intestinal disease associated with diarrhea and colitis. C. difficile associated disease (CDAD) is linked with antibiotic treatment regimes and is increasing in incidence, with many hospital associated (nosocomial) outbreaks and continued sequelae. Current theory implies that clinical treatment with antibiotics for other infections disturbs the normal intestinal flora, alloing C. difficile to become established as an invader. While there is evidence to support this etiology, the details of how bacterial overgrowth happens, why many patients do not recover fully after treatment and why, in some patients, CDAD recurs, is still unknown. It is important to examine in detail the changes to the intestinal microbiome that contribute to disease caused by opportunistic pathogens such as C. difficile, as well as to elucidate potential interactions between the intestinal microbiome and pathogens. The language used to describe C. difficile overgrowth in the intestine is similar to that used by invasion ecologists to describe invasion events in large ecosystems. By considering the intestinal microbiome as an ecosystem and combining techniques commonly used in microbial ecology with sampling and analysis techniques from invasion and landscape ecology, a better understanding of how opportunistic pathogens invade and cause disease can be achieved. Use of a recently developed mouse model combined with deep sequencing analysis of different intestinal compartments will determine if C. difficile is distributed non- randomly with regard to location and bacterial taxa i the GI tract, and whether these bacterial associations affect where C. difficile is active which of its various disease states is manifested. In addition, fluorescence in situ hybridization (FISH) wil be used to perform a detailed analysis of the spatial organization of C. difficile with respect to specific microbiome taxa during disease progression and treatment. Aim 1: Comparison using deep sequencing and metagenomic analysis of bacterial communities in five different areas of the intestine, during antibiotic therapy, during the different states of CDAD and in normal controls. Aim 2: Spatial mapping of bacterial populations within the intestine using FISH with a special emphasis on individual species that have positive and negative associations with C. difficile. Aim 3: Advancing the NIAID AREA mission will be accomplished by uniting a molecular microbial ecologist, a bioinformatician and a veterinarian (also a Ph.D. candidate), all of whom are new NIH Investigators, in this small-scale, health-related research project which will develop and implement novel research approaches to study fundamental aspects of infectious disease.

Over a three-year period, this International Research Experience for Students (IRES) program will engage two U.S. undergraduate and two U.S. graduate students annually, for a total of twelve participants, at research sites in Greenland and Denmark to study Arctic microbiology and biogeochemistry under multiple climate change scenarios. Following required training and research preparation at the University of Montana, students travel to Copenhagen for orientation and introduction to international mentors before they depart for three weeks of field work in Greenland. Throughout, students are co-mentored by William Holben, the U.S. principal investigator (PI), and a team of experts associated with the Greenlandic Center for Permafrost Studies (CENPERM), a center that is administered by the University of Copenhagen and the Geological Survey of Denmark and Greenland. Each student's research training will include experience with planning and implementing field strategies for permafrost, ice sheet, and hot spring and glacier sampling in a way that promotes student ownership of individual projects, while facilitating the integration of multiple data sets obtained throughout the duration of this IRES activity. Results are expected to contribute to what is known about thawing permafrost and accelerated microbial decomposition of large amounts of organic matter stored in Arctic ecosystems.

Following each season of fieldwork and sample processing in Greenland, participants return to Copenhagen to prepare collected samples for metagenomic DNA and mRNA sequencing and bioinformatic analysis. These will be studied for patterns of microbial community change that reflect differing and changing environmental parameters. Upon returning to Montana students will continue the computational and bioinformatic aspects of their studies. Results should provide new insights into microbial community structure and activities on sheet ice and glaciers, as well as microbial biogeochemical cycling contributions to greenhouse gas emissions from permafrost soils. Over the course of this IRES program, the U.S. and CENPERM partners expect to deepen their collaboration through international teamwork, research training, and cultural interaction, as they mentor and engage a cadre of diverse students, including Native Americans, to become the next generation of climate change experts. For broader impact, all participating U.S. students will benefit from early career experience with the kind of long-term relationship, professional network and research collaboration that is increasingly necessary to address complex global ecological issues.